If you are FM quilting, I'm assuming you're using a FM or hopping foot, and have your feed dogs down or disengaged. In that case, the machine should not be feeding the fabric at all, it is the motion of your hands that moves the fabric. So what might be happening is the FM foot is not hopping high enough to clear the extra-thick seam.

Some machines have the ability to adjust the amount of pressure on the pressure foot. If yours does, you can lessen that pressure so there is more 'give' when pushing that thick seam underneath.

If not, you may have to avoid the seams, or, and this will sound funny, take the quilt sandwich and hammer those seam intersections flat. There was actually a vendor at a quilt show once selling rubber mallets for hammering down seam allowances!

I try to get my seam allowances to lay as flat as possible. Sometimes if there are lots that come together in the same spot, I try to adjust my FMQ design so I don't have to stitch over those spots. My machine will go over them but the stitch size does change and I will occasionally get a skipped stitch. I just avoid them whenever possible.

If not, you may have to avoid the seams, or, and this will sound funny, take the quilt sandwich and hammer those seam intersections flat. There was actually a vendor at a quilt show once selling rubber mallets for hammering down seam allowances!

I saw Liz Porter do it on a Fons and Porter episode once! It is really helpful when you have lots of seams meeting together like when you are making a star block or sometimes with a pinwheel block. I have a hammer in my sewing room just for this purpose. Have had to pull it out a time or two.

No one has ever become poor by giving. - Anne Frank
Darkness cannot drive out darkness; only light can do that. Hate cannot drive out hate; only love can do that. - Martin Luther King, Jr.

You will be surprised at the difference a little hammering can make on thick seams. Be sure and place the area to be hammered on a hard surface when you hammer it. A soft surface just cushions the blows.

I don't understand how your machine can be "feeding" your material if you are FMQing. Your feed dogs should be down and you should be controlling the speed of the flow of material. Also make sure you have a FMQ food on the machine. Hopefully you will get this problem figured out.